Comparison of two molecular diagnostic methods for identifying Beijing genotype of Mycobacterium tuberculosis
Abstract
Background and Objectives: The Beijing family of Mycobacterium tuberculosis has been identified as a severe pathogen among this species and found in many clinical isolates during the last decade. Early identification of such genotype is important for better prevention and treatment of tuberculosis. The present study performed to compare the efficiency of Real-Time PCR and IS6110-Based Inverse PCR methods to identify the Beijing family.
Materials and Methods: This study was carried out on 173 clinical isolates of Mycobacterium tuberculosis complex in Golestan Province, northern Iran. DNA extraction performed by boiling and determining the Beijing and non-Beijing strains carried out using Real-Time PCR and IS6110-Based Inverse PCR.
Results: In both Real-Time PCR and IS6110-Based Inverse PCR method, 24 specimens (13.9%) of the Beijing family were identified and the result of the IS6110-Based Inverse PCR method showed that all the Beijing strains in this region belonged to the Ancient Beijing sub-lineage.
Conclusion: Although the efficacy of the two methods in the diagnosis of the Beijing family is similar, the IS6110-Based Inverse PCR is more applicable to the ability to detect new and old Beijing family.
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11. Pasechnik O, Vyazovaya A, Vitriv S, Tatarintseva M, Blokh A, Stasenko V, et al. Major genotype families and epidemic clones of Mycobacterium tuberculosis in Omsk region, Western Siberia, Russia, marked by a high burden of tuberculosis-HIV coinfection. Tuberculosis 2018;108:163-168.
12. Hanekom M, Van Der Spuy G, Streicher E, Ndabambi S, McEvoy C, Kidd M, et al. A recently evolved sublineage of the Mycobacterium tuberculosis Beijing strain family is associated with an increased ability to spread and cause disease. J Clin Microbiol 2007;45:1483-1490.
13. Huyen MN, Buu TN, Tiemersma E, Lan NT, Dung NH, Kremer K, et al. Tuberculosis relapse in Vietnam is significantly associated with Mycobacterium tuberculosis Beijing genotype infections. J Infect Dis 2013;207:1516-1524.
14. Bifani PJ, Mathema B, Kurepina NE, Kreiswirth BN. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol 2002;10:45-52.
15. Erie H, Kaboosi H, Javid N, Shirzad-Aski H, Taziki M, Kuchaksaraee MB, et al. The high prevalence of Mycobacterium tuberculosis Beijing strain at an early age and extra-pulmonary tuberculosis cases. Iran J Microbiol 2017;9:312-317.
16. Ribeiro SC, Gomes LL, Amaral EP, Andrade MR, Almeida FM, Rezende AL, et al. Mycobacterium tuberculosis strains of the modern sublineage of the Beijing family are more likely to display increased virulence than strains of the ancient sublineage. J Clin Microbiol 2014;52:2615-2624.
17. Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015;47:242-249.
18. Devi KR, Bhutia R, Bhowmick S, Mukherjee K, Mahanta J, Narain K. Genetic diversity of Mycobacterium tuberculosis isolates from Assam, India: dominance of Beijing family and discovery of two new clades related to CAS1_Delhi and EAI family based on spoligotyping and MIRU-VNTR typing. PLoS One 2015;10(12): e0145860.
19. Chakraborty P, Kulkarni S, Rajan R, Sainis K. Mycobacterium tuberculosis strains from ancient and modern lineages induce distinct patterns of immune responses. J Infect Dev Ctries 2018;11:904-911.
20. Liu Q, Luo T, Dong X, Sun G, Liu Z, Gan M, et al. Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. Emerg Microbes Infect 2016;5(2):e14.
21. Iwamoto T, Fujiyama R, Yoshida S, Wada T, Shirai C, Kawakami Y. Population structure dynamics of Mycobacterium tuberculosis Beijing strains during past decades in Japan. J Clin Microbiol 2009;47:3340-3343.
22. Kochkaksaraei MB, Kaboosi H, Ghaemi EA. Genetic variation of the Mycobacterium tuberculosis in north of Iran; the Golestan Province. Iran Red Crescent Med J 2019; 21 (8); e91553.
23. Shafipour M, Ghane M, Alang SR, Livani S, Javid N, Shakeri F. Non tuberculosis Mycobacteria isolated from tuberculosis patients in Golestan province, North of Iran. Ann Biol Res 2013;4:133-137.
24. Hillemann D, Warren R, Kubica T, Rüsch-Gerdes S, Niemann S. Rapid detection of Mycobacterium tuberculosis Beijing genotype strains by real-time PCR. J Clin Microbiol 2006;44:302-306.
25. Mokrousov I, Jiao WW, Valcheva V, Vyazovaya A, Otten T, Ly HM, et al. Rapid detection of the Mycobacterium tuberculosis Beijing genotype and its ancient and modern sublineages by IS6110-Based Inverse PCR. J Clin Microbiol 2006;44:2851-2856.
26. Mirbagheri SZ, Meshkat Z, Naderinasab M, Ghadamsoltani T, Rostami S, Heravi MM, et al. Frequency of Beijing family of Mycobacterium tuberculosis in Mashhad, Northeast of Iran. Arch Med Lab Sci 2016;2:102-107.
27. Hoffner S, Sahebi L, Ansarin K, Sabour S, Mohajeri P. Mycobacterium tuberculosis of the Beijing genotype in Iran and the World Health Organization Eastern Mediterranean Region: a meta-analysis. Microb Drug Resist 2018;24:693-698.
28. Doroudchi M, Kremer K, Basiri EA, Kadivar MR, Van Soolingen D, Ghaderi AA. IS6110-RFLP and spoligotyping of Mycobacterium tuberculosis isolates in Iran. Scand J Infect Dis 2000;32:663-668.
29. Farnia P, Masjedi MR, Mirsaeidi M, Mohammadi F, Vincent V, Bahadori M, et al. Prevalence of Haarlem I and Beijing types of Mycobacterium tuberculosis strains in Iranian and Afghan MDR-TB patients. J Infect 2006;53:331-336.
30. Velayati AA, Farnia P, Mirsaeidi M, Reza Masjedi M. The most prevalent Mycobacterium tuberculosis superfamilies among Iranian and Afghan TB cases. Scand J Infect Dis 2006;38:463-468.
31. Rohani M, Farnia P, Nasab MN, Moniri R, Torfeh M, Amiri M. Beijing genotype and other predominant Mycobacterium tuberculosis spoligotypes observed in Mashhad city, Iran. Indian J Med Microbiol 2009;27:306-310.
32. Kazempour M, Masjedi M, Velayati A, Tajeddin E, Farnia P, Kargar M, et al. Identification of Mycobacterium tuberculosis beijing genotype using three different molecular methods. Koomesh 2009;11:7-14.
33. Mozafari M, Farnia P, Jafarian M, Razavi Deligani M, Kazempour M, Masjedi M, et al. Comparison of Mycobacterium tuberculosis Beijing genotype with other Mycobacterium tuberculosis strains Using MIRU-VNTR method. Iran South Med J 2012;15:1-12.
34. Khosravi AD, Goodarzi H, Alavi SM, Akhond MR. Application of deletion-targeted multiplex PCR technique for detection of Mycobacterium tuberculosis Beijing strains in samples from tuberculosis patients. Iran J Microbiol 2014;6: 330-334.
35. Mohajeri P, Moradi S, Atashi S, Farahani A. Mycobacterium tuberculosis Beijing genotype in western Iran: Distribution and drug resistance. Journal of clinical and diagnostic research. J Clin Diagn Res 2016;10: DC05-DC07.
36. Schürch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, et al. Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype. Infect Genet Evol 2011;11:587-597.
2. Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 2013;45: 1176-1182.
3. Firdessa R, Berg S, Hailu E, Schelling E, Gumi B, Erenso G, et al. Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg Infect Dis 2013;19: 460-463.
4. Arif HM, Hussain Z. Prevalence of Mycobacterium tuberculosis Beijing strains in Punjab Pakistan. Int J Curr Res Aca Rev 2014;2:74-82.
5. Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, et al. Genome-wide analysis of multi-and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018;50:307-316.
6. Roycroft E, O'Toole R, Fitzgibbon M, Montgomery L, O'Meara M, Downes P, et al. Molecular epidemiology of multi-and extensively-drug-resistant Mycobacterium tuberculosis in Ireland, 2001–2014. J Infect 2018;76:55-67.
7. Bainomugisa A, Duarte T, Lavu E, Pandey S, Coulter C, Marais B, et al. A complete nanonpore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel genetic variation in repetitive PE/PPE gene regions. Microbial genom 2018; 4. doi: 10.1099/mgen.0.000188.
8. Mokrousov I, Chernyaeva E, Vyazovaya A, Skiba Y, Solovieva N, Valcheva V, et al. Rapid assay for detection of the epidemiologically important central Asian/Russian strain of the Mycobacterium tuberculosis Beijing genotype. J Clin Microbiol 2018;56(2):e01551-17.
9. Lasunskaia E, Ribeiro SC, Manicheva O, Gomes LL, Suffys PN, Mokrousov I, et al. Emerging multidrug resistant Mycobacterium tuberculosis strains of the Beijing genotype circulating in Russia express a pattern of biological properties associated with enhanced virulence. Microbes Infect 2010;12:467-475.
10. Buu TN, Huyen M, Lan N, Quy H, Hen N, Zignol M, et al. The Beijing genotype is associated with young age and multidrug-resistant tuberculosis in rural Vietnam. Int J Tuberc Lung Dis 2009;13:900-906.
11. Pasechnik O, Vyazovaya A, Vitriv S, Tatarintseva M, Blokh A, Stasenko V, et al. Major genotype families and epidemic clones of Mycobacterium tuberculosis in Omsk region, Western Siberia, Russia, marked by a high burden of tuberculosis-HIV coinfection. Tuberculosis 2018;108:163-168.
12. Hanekom M, Van Der Spuy G, Streicher E, Ndabambi S, McEvoy C, Kidd M, et al. A recently evolved sublineage of the Mycobacterium tuberculosis Beijing strain family is associated with an increased ability to spread and cause disease. J Clin Microbiol 2007;45:1483-1490.
13. Huyen MN, Buu TN, Tiemersma E, Lan NT, Dung NH, Kremer K, et al. Tuberculosis relapse in Vietnam is significantly associated with Mycobacterium tuberculosis Beijing genotype infections. J Infect Dis 2013;207:1516-1524.
14. Bifani PJ, Mathema B, Kurepina NE, Kreiswirth BN. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol 2002;10:45-52.
15. Erie H, Kaboosi H, Javid N, Shirzad-Aski H, Taziki M, Kuchaksaraee MB, et al. The high prevalence of Mycobacterium tuberculosis Beijing strain at an early age and extra-pulmonary tuberculosis cases. Iran J Microbiol 2017;9:312-317.
16. Ribeiro SC, Gomes LL, Amaral EP, Andrade MR, Almeida FM, Rezende AL, et al. Mycobacterium tuberculosis strains of the modern sublineage of the Beijing family are more likely to display increased virulence than strains of the ancient sublineage. J Clin Microbiol 2014;52:2615-2624.
17. Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015;47:242-249.
18. Devi KR, Bhutia R, Bhowmick S, Mukherjee K, Mahanta J, Narain K. Genetic diversity of Mycobacterium tuberculosis isolates from Assam, India: dominance of Beijing family and discovery of two new clades related to CAS1_Delhi and EAI family based on spoligotyping and MIRU-VNTR typing. PLoS One 2015;10(12): e0145860.
19. Chakraborty P, Kulkarni S, Rajan R, Sainis K. Mycobacterium tuberculosis strains from ancient and modern lineages induce distinct patterns of immune responses. J Infect Dev Ctries 2018;11:904-911.
20. Liu Q, Luo T, Dong X, Sun G, Liu Z, Gan M, et al. Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. Emerg Microbes Infect 2016;5(2):e14.
21. Iwamoto T, Fujiyama R, Yoshida S, Wada T, Shirai C, Kawakami Y. Population structure dynamics of Mycobacterium tuberculosis Beijing strains during past decades in Japan. J Clin Microbiol 2009;47:3340-3343.
22. Kochkaksaraei MB, Kaboosi H, Ghaemi EA. Genetic variation of the Mycobacterium tuberculosis in north of Iran; the Golestan Province. Iran Red Crescent Med J 2019; 21 (8); e91553.
23. Shafipour M, Ghane M, Alang SR, Livani S, Javid N, Shakeri F. Non tuberculosis Mycobacteria isolated from tuberculosis patients in Golestan province, North of Iran. Ann Biol Res 2013;4:133-137.
24. Hillemann D, Warren R, Kubica T, Rüsch-Gerdes S, Niemann S. Rapid detection of Mycobacterium tuberculosis Beijing genotype strains by real-time PCR. J Clin Microbiol 2006;44:302-306.
25. Mokrousov I, Jiao WW, Valcheva V, Vyazovaya A, Otten T, Ly HM, et al. Rapid detection of the Mycobacterium tuberculosis Beijing genotype and its ancient and modern sublineages by IS6110-Based Inverse PCR. J Clin Microbiol 2006;44:2851-2856.
26. Mirbagheri SZ, Meshkat Z, Naderinasab M, Ghadamsoltani T, Rostami S, Heravi MM, et al. Frequency of Beijing family of Mycobacterium tuberculosis in Mashhad, Northeast of Iran. Arch Med Lab Sci 2016;2:102-107.
27. Hoffner S, Sahebi L, Ansarin K, Sabour S, Mohajeri P. Mycobacterium tuberculosis of the Beijing genotype in Iran and the World Health Organization Eastern Mediterranean Region: a meta-analysis. Microb Drug Resist 2018;24:693-698.
28. Doroudchi M, Kremer K, Basiri EA, Kadivar MR, Van Soolingen D, Ghaderi AA. IS6110-RFLP and spoligotyping of Mycobacterium tuberculosis isolates in Iran. Scand J Infect Dis 2000;32:663-668.
29. Farnia P, Masjedi MR, Mirsaeidi M, Mohammadi F, Vincent V, Bahadori M, et al. Prevalence of Haarlem I and Beijing types of Mycobacterium tuberculosis strains in Iranian and Afghan MDR-TB patients. J Infect 2006;53:331-336.
30. Velayati AA, Farnia P, Mirsaeidi M, Reza Masjedi M. The most prevalent Mycobacterium tuberculosis superfamilies among Iranian and Afghan TB cases. Scand J Infect Dis 2006;38:463-468.
31. Rohani M, Farnia P, Nasab MN, Moniri R, Torfeh M, Amiri M. Beijing genotype and other predominant Mycobacterium tuberculosis spoligotypes observed in Mashhad city, Iran. Indian J Med Microbiol 2009;27:306-310.
32. Kazempour M, Masjedi M, Velayati A, Tajeddin E, Farnia P, Kargar M, et al. Identification of Mycobacterium tuberculosis beijing genotype using three different molecular methods. Koomesh 2009;11:7-14.
33. Mozafari M, Farnia P, Jafarian M, Razavi Deligani M, Kazempour M, Masjedi M, et al. Comparison of Mycobacterium tuberculosis Beijing genotype with other Mycobacterium tuberculosis strains Using MIRU-VNTR method. Iran South Med J 2012;15:1-12.
34. Khosravi AD, Goodarzi H, Alavi SM, Akhond MR. Application of deletion-targeted multiplex PCR technique for detection of Mycobacterium tuberculosis Beijing strains in samples from tuberculosis patients. Iran J Microbiol 2014;6: 330-334.
35. Mohajeri P, Moradi S, Atashi S, Farahani A. Mycobacterium tuberculosis Beijing genotype in western Iran: Distribution and drug resistance. Journal of clinical and diagnostic research. J Clin Diagn Res 2016;10: DC05-DC07.
36. Schürch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, et al. Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype. Infect Genet Evol 2011;11:587-597.
| Files | ||
| Issue | Vol 12 No 3 (2020) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v12i3.3238 | |
| Keywords | ||
| Mycobacterium tuberculosis; Real-time polymerase chain reaction; Beijing family | ||
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How to Cite
1.
Mahghani GA, Kargar M, Kafilzadeh F, Davoodi H, Ghaemi EA. Comparison of two molecular diagnostic methods for identifying Beijing genotype of Mycobacterium tuberculosis. Iran J Microbiol. 2020;12(3):209-215.
